gnu/packages/machine-learning.scm

   1 ;;; GNU Guix --- Functional package management for GNU
   2 ;;; Copyright © 2015, 2016, 2017 Ricardo Wurmus <rekado@elephly.net>
   3 ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il>
   4 ;;; Copyright © 2016, 2017 Marius Bakke <mbakke@fastmail.com>
   5 ;;; Copyright © 2016 Hartmut Goebel <h.goebel@crazy-compilers.com>
   6 ;;; Copyright © 2018 Tobias Geerinckx-Rice <me@tobias.gr>
   7 ;;; Copyright © 2018 Mark Meyer <mark@ofosos.org>
   8 ;;; Copyright © 2018 Ben Woodcroft <donttrustben@gmail.com>
   9 ;;;
  10 ;;; This file is part of GNU Guix.
  11 ;;;
  12 ;;; GNU Guix is free software; you can redistribute it and/or modify it
  13 ;;; under the terms of the GNU General Public License as published by
  14 ;;; the Free Software Foundation; either version 3 of the License, or (at
  15 ;;; your option) any later version.
  16 ;;;
  17 ;;; GNU Guix is distributed in the hope that it will be useful, but
  18 ;;; WITHOUT ANY WARRANTY; without even the implied warranty of
  19 ;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  20 ;;; GNU General Public License for more details.
  21 ;;;
  22 ;;; You should have received a copy of the GNU General Public License
  23 ;;; along with GNU Guix.  If not, see <http://www.gnu.org/licenses/>.
  24
  25 (define-module (gnu packages machine-learning)
  26   #:use-module ((guix licenses) #:prefix license:)
  27   #:use-module (guix packages)
  28   #:use-module (guix utils)
  29   #:use-module (guix download)
  30   #:use-module (guix svn-download)
  31   #:use-module (guix build-system cmake)
  32   #:use-module (guix build-system gnu)
  33   #:use-module (guix build-system ocaml)
  34   #:use-module (guix build-system python)
  35   #:use-module (guix build-system r)
  36   #:use-module (guix git-download)
  37   #:use-module (gnu packages)
  38   #:use-module (gnu packages autotools)
  39   #:use-module (gnu packages boost)
  40   #:use-module (gnu packages check)
  41   #:use-module (gnu packages compression)
  42   #:use-module (gnu packages cran)
  43   #:use-module (gnu packages dejagnu)
  44   #:use-module (gnu packages gcc)
  45   #:use-module (gnu packages image)
  46   #:use-module (gnu packages maths)
  47   #:use-module (gnu packages ocaml)
  48   #:use-module (gnu packages perl)
  49   #:use-module (gnu packages pkg-config)
  50   #:use-module (gnu packages python)
  51   #:use-module (gnu packages statistics)
  52   #:use-module (gnu packages swig)
  53   #:use-module (gnu packages xml)
  54   #:use-module (gnu packages xorg))
  55
  56 (define-public fann
  57   ;; The last release is >100 commits behind, so we package from git.
  58   (let ((commit "d71d54788bee56ba4cf7522801270152da5209d7"))
  59     (package
  60       (name "fann")
  61       (version (string-append "2.2.0-1." (string-take commit 8)))
  62       (source (origin
  63                 (method git-fetch)
  64                 (uri (git-reference
  65                       (url "https://github.com/libfann/fann.git")
  66                       (commit commit)))
  67                 (file-name (string-append name "-" version "-checkout"))
  68                 (sha256
  69                  (base32
  70                   "0ibwpfrjs6q2lijs8slxjgzb2llcl6rk3v2ski4r6215g5jjhg3x"))))
  71       (build-system cmake-build-system)
  72       (arguments
  73        `(#:phases
  74          (modify-phases %standard-phases
  75            (replace 'check
  76              (lambda* (#:key outputs #:allow-other-keys)
  77                (let* ((out (assoc-ref outputs "out")))
  78                  (with-directory-excursion (string-append (getcwd) "/tests")
  79                    (invoke "./fann_tests"))))))))
  80       (home-page "http://leenissen.dk/fann/wp/")
  81       (synopsis "Fast Artificial Neural Network")
  82       (description
  83        "FANN is a free open source neural network library, which implements
  84 multilayer artificial neural networks in C with support for both fully
  85 connected and sparsely connected networks.")
  86       (license license:lgpl2.1))))
  87
  88 (define-public libsvm
  89   (package
  90     (name "libsvm")
  91     (version "3.22")
  92     (source
  93      (origin
  94        (method url-fetch)
  95        (uri (string-append "https://www.csie.ntu.edu.tw/~cjlin/libsvm/"
  96                            name "-" version ".tar.gz"))
  97        (sha256
  98         (base32
  99          "0zd7s19y5vb7agczl6456bn45cj1y64739sslaskw1qk7dywd0bd"))))
 100     (build-system gnu-build-system)
 101     (arguments
 102      `(#:tests? #f ;no "check" target
 103        #:phases (modify-phases %standard-phases
 104                   (delete 'configure)
 105                   (replace
 106                    'install             ; no ‘install’ target
 107                    (lambda* (#:key outputs #:allow-other-keys)
 108                      (let* ((out (assoc-ref outputs "out"))
 109                             (bin (string-append out "/bin/")))
 110                        (mkdir-p bin)
 111                        (for-each (lambda (file)
 112                                    (copy-file file (string-append bin file)))
 113                                  '("svm-train"
 114                                    "svm-predict"
 115                                    "svm-scale")))
 116                      #t)))))
 117     (home-page "http://www.csie.ntu.edu.tw/~cjlin/libsvm/")
 118     (synopsis "Library for Support Vector Machines")
 119     (description
 120      "LIBSVM is a machine learning library for support vector
 121 classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and
 122 distribution estimation (one-class SVM).  It supports multi-class
 123 classification.")
 124     (license license:bsd-3)))
 125
 126 (define-public python-libsvm
 127   (package (inherit libsvm)
 128     (name "python-libsvm")
 129     (build-system gnu-build-system)
 130     (arguments
 131      `(#:tests? #f ;no "check" target
 132        #:make-flags '("-C" "python")
 133        #:phases
 134        (modify-phases %standard-phases
 135          (delete 'configure)
 136          (replace
 137           'install                      ; no ‘install’ target
 138           (lambda* (#:key inputs outputs #:allow-other-keys)
 139             (let ((site (string-append (assoc-ref outputs "out")
 140                                        "/lib/python"
 141                                        (string-take
 142                                         (string-take-right
 143                                          (assoc-ref inputs "python") 5) 3)
 144                                        "/site-packages/")))
 145               (substitute* "python/svm.py"
 146                 (("../libsvm.so.2") "libsvm.so.2"))
 147               (mkdir-p site)
 148               (for-each (lambda (file)
 149                           (copy-file file (string-append site (basename file))))
 150                         (find-files "python" "\\.py"))
 151               (copy-file "libsvm.so.2"
 152                          (string-append site "libsvm.so.2")))
 153             #t)))))
 154     (inputs
 155      `(("python" ,python)))
 156     (synopsis "Python bindings of libSVM")))
 157
 158 (define-public ghmm
 159   ;; The latest release candidate is several years and a couple of fixes have
 160   ;; been published since.  This is why we download the sources from the SVN
 161   ;; repository.
 162   (let ((svn-revision 2341))
 163     (package
 164       (name "ghmm")
 165       (version (string-append "0.9-rc3-0." (number->string svn-revision)))
 166       (source (origin
 167                 (method svn-fetch)
 168                 (uri (svn-reference
 169                       (url "http://svn.code.sf.net/p/ghmm/code/trunk")
 170                       (revision svn-revision)))
 171                 (file-name (string-append name "-" version))
 172                 (sha256
 173                  (base32
 174                   "0qbq1rqp94l530f043qzp8aw5lj7dng9wq0miffd7spd1ff638wq"))))
 175       (build-system gnu-build-system)
 176       (arguments
 177        `(#:imported-modules (,@%gnu-build-system-modules
 178                              (guix build python-build-system))
 179          #:phases
 180          (modify-phases %standard-phases
 181            (add-after 'unpack 'enter-dir
 182              (lambda _ (chdir "ghmm") #t))
 183            (delete 'check)
 184            (add-after 'install 'check
 185              (assoc-ref %standard-phases 'check))
 186            (add-before 'check 'fix-PYTHONPATH
 187              (lambda* (#:key inputs outputs #:allow-other-keys)
 188                (let ((python-version ((@@ (guix build python-build-system)
 189                                            get-python-version)
 190                                       (assoc-ref inputs "python"))))
 191                  (setenv "PYTHONPATH"
 192                          (string-append (getenv "PYTHONPATH")
 193                                         ":" (assoc-ref outputs "out")
 194                                         "/lib/python" python-version
 195                                         "/site-packages")))
 196                #t))
 197            (add-after 'enter-dir 'fix-runpath
 198              (lambda* (#:key outputs #:allow-other-keys)
 199                (substitute* "ghmmwrapper/setup.py"
 200                  (("^(.*)extra_compile_args = \\[" line indent)
 201                   (string-append indent
 202                                  "extra_link_args = [\"-Wl,-rpath="
 203                                  (assoc-ref outputs "out") "/lib\"],\n"
 204                                  line
 205                                  "\"-Wl,-rpath="
 206                                  (assoc-ref outputs "out")
 207                                  "/lib\", ")))
 208                #t))
 209            (add-after 'enter-dir 'disable-broken-tests
 210              (lambda _
 211                (substitute* "tests/Makefile.am"
 212                  ;; GHMM_SILENT_TESTS is assumed to be a command.
 213                  (("TESTS_ENVIRONMENT.*") "")
 214                  ;; Do not build broken tests.
 215                  (("chmm .*") "")
 216                  (("read_fa .*") "")
 217                  (("mcmc .*") "")
 218                  (("label_higher_order_test.*$")
 219                   "label_higher_order_test\n"))
 220
 221                ;; These Python unittests are broken as there is no gato.
 222                ;; See https://sourceforge.net/p/ghmm/support-requests/3/
 223                (substitute* "ghmmwrapper/ghmmunittests.py"
 224                  (("^(.*)def (testNewXML|testMultipleTransitionClasses|testNewXML)"
 225                    line indent)
 226                   (string-append indent
 227                                  "@unittest.skip(\"Disabled by Guix\")\n"
 228                                  line)))
 229                #t))
 230            (add-after 'disable-broken-tests 'autogen
 231              (lambda _
 232                (zero? (system* "bash" "autogen.sh")))))))
 233       (inputs
 234        `(("python" ,python-2) ; only Python 2 is supported
 235          ("libxml2" ,libxml2)))
 236       (native-inputs
 237        `(("pkg-config" ,pkg-config)
 238          ("dejagnu" ,dejagnu)
 239          ("swig" ,swig)
 240          ("autoconf" ,autoconf)
 241          ("automake" ,automake)
 242          ("libtool" ,libtool)))
 243       (home-page "http://ghmm.org")
 244       (synopsis "Hidden Markov Model library")
 245       (description
 246        "The General Hidden Markov Model library (GHMM) is a C library with
 247 additional Python bindings implementing a wide range of types of @dfn{Hidden
 248 Markov Models} (HMM) and algorithms: discrete, continuous emissions, basic
 249 training, HMM clustering, HMM mixtures.")
 250       (license license:lgpl2.0+))))
 251
 252 (define-public mcl
 253   (package
 254     (name "mcl")
 255     (version "14.137")
 256     (source (origin
 257               (method url-fetch)
 258               (uri (string-append
 259                     "http://micans.org/mcl/src/mcl-"
 260                     (string-replace-substring version "." "-")
 261                     ".tar.gz"))
 262               (sha256
 263                (base32
 264                 "15xlax3z31lsn62vlg94hkm75nm40q4679amnfg13jm8m2bnhy5m"))))
 265     (build-system gnu-build-system)
 266     (arguments
 267      `(#:configure-flags (list "--enable-blast")))
 268     (inputs
 269      `(("perl" ,perl)))
 270     (home-page "http://micans.org/mcl/")
 271     (synopsis "Clustering algorithm for graphs")
 272     (description
 273      "The MCL algorithm is short for the @dfn{Markov Cluster Algorithm}, a
 274 fast and scalable unsupervised cluster algorithm for graphs (also known as
 275 networks) based on simulation of (stochastic) flow in graphs.")
 276     ;; In the LICENCE file and web page it says "The software is licensed
 277     ;; under the GNU General Public License, version 3.", but in several of
 278     ;; the source code files it suggests GPL3 or later.
 279     ;; http://listserver.ebi.ac.uk/pipermail/mcl-users/2016/000376.html
 280     (license license:gpl3)))
 281
 282 (define-public ocaml-mcl
 283   (package
 284     (name "ocaml-mcl")
 285     (version "12-068oasis4")
 286     (source
 287      (origin
 288        (method url-fetch)
 289        (uri (string-append
 290              "https://github.com/fhcrc/mcl/archive/"
 291              version ".tar.gz"))
 292        (file-name (string-append name "-" version ".tar.gz"))
 293        (sha256
 294         (base32
 295          "1l5jbhwjpsj38x8b9698hfpkv75h8hn3kj0gihjhn8ym2cwwv110"))))
 296     (build-system ocaml-build-system)
 297     (arguments
 298      `(#:phases
 299        (modify-phases %standard-phases
 300          (add-before 'configure 'patch-paths
 301            (lambda _
 302              (substitute* "configure"
 303                (("SHELL = /bin/sh") (string-append "SHELL = "(which "sh"))))
 304              (substitute* "setup.ml"
 305                (("LDFLAGS=-fPIC")
 306                 (string-append "LDFLAGS=-fPIC\"; \"SHELL=" (which "sh"))))
 307              #t)))))
 308     (home-page "https://github.com/fhcrc/mcl")
 309     (synopsis "OCaml wrappers around MCL")
 310     (description
 311      "This package provides OCaml bindings for the MCL graph clustering
 312 algorithm.")
 313     (license license:gpl3)))
 314
 315 (define-public ocaml4.01-mcl
 316   (package-with-ocaml4.01 ocaml-mcl))
 317
 318 (define-public randomjungle
 319   (package
 320     (name "randomjungle")
 321     (version "2.1.0")
 322     (source
 323      (origin
 324        (method url-fetch)
 325        (uri (string-append
 326              "http://www.imbs-luebeck.de/imbs/sites/default/files/u59/"
 327              "randomjungle-" version ".tar_.gz"))
 328        (sha256
 329         (base32
 330          "12c8rf30cla71swx2mf4ww9mfd8jbdw5lnxd7dxhyw1ygrvg6y4w"))))
 331     (build-system gnu-build-system)
 332     (arguments
 333      `(#:configure-flags
 334        (list (string-append "--with-boost="
 335                             (assoc-ref %build-inputs "boost")))
 336        #:phases
 337        (modify-phases %standard-phases
 338          (add-before
 339           'configure 'set-CXXFLAGS
 340           (lambda _
 341             (setenv "CXXFLAGS" "-fpermissive ")
 342             #t)))))
 343     (inputs
 344      `(("boost" ,boost)
 345        ("gsl" ,gsl)
 346        ("libxml2" ,libxml2)
 347        ("zlib" ,zlib)))
 348     (native-inputs
 349      `(("gfortran" ,gfortran)
 350        ("gfortran:lib" ,gfortran "lib")))
 351     ;; Non-portable assembly instructions are used so building fails on
 352     ;; platforms other than x86_64 or i686.
 353     (supported-systems '("x86_64-linux" "i686-linux"))
 354     (home-page "http://www.imbs-luebeck.de/imbs/de/node/227/")
 355     (synopsis "Implementation of the Random Forests machine learning method")
 356     (description
 357      "Random Jungle is an implementation of Random Forests.  It is supposed to
 358 analyse high dimensional data.  In genetics, it can be used for analysing big
 359 Genome Wide Association (GWA) data.  Random Forests is a powerful machine
 360 learning method.  Most interesting features are variable selection, missing
 361 value imputation, classifier creation, generalization error estimation and
 362 sample proximities between pairs of cases.")
 363     (license license:gpl3+)))
 364
 365 (define-public shogun
 366   (package
 367     (name "shogun")
 368     (version "4.0.0")
 369     (source
 370      (origin
 371        (method url-fetch)
 372        (uri (string-append
 373              "ftp://shogun-toolbox.org/shogun/releases/"
 374              (version-major+minor version)
 375              "/sources/shogun-" version ".tar.bz2"))
 376        (sha256
 377         (base32
 378          "159nlijnb7mnrv9za80wnm1shwvy45hgrqzn51hxy7gw4z6d6fdb"))
 379        (modules '((guix build utils)
 380                   (ice-9 rdelim)))
 381        (snippet
 382         '(begin
 383            ;; Remove non-free sources and files referencing them
 384            (for-each delete-file
 385                      (find-files "src/shogun/classifier/svm/"
 386                                  "SVMLight\\.(cpp|h)"))
 387            (for-each delete-file
 388                      (find-files "examples/undocumented/libshogun/"
 389                                  (string-append
 390                                   "(classifier_.*svmlight.*|"
 391                                   "evaluation_cross_validation_locked_comparison).cpp")))
 392            ;; Remove non-free functions.
 393            (define (delete-ifdefs file)
 394              (with-atomic-file-replacement file
 395                (lambda (in out)
 396                  (let loop ((line (read-line in 'concat))
 397                             (skipping? #f))
 398                    (if (eof-object? line)
 399                        #t
 400                        (let ((skip-next?
 401                               (or (and skipping?
 402                                        (not (string-prefix?
 403                                              "#endif //USE_SVMLIGHT" line)))
 404                                   (string-prefix?
 405                                    "#ifdef USE_SVMLIGHT" line))))
 406                          (when (or (not skipping?)
 407                                    (and skipping? (not skip-next?)))
 408                            (display line out))
 409                          (loop (read-line in 'concat) skip-next?)))))))
 410            (for-each delete-ifdefs (find-files "src/shogun/kernel/"
 411                                                "^Kernel\\.(cpp|h)"))))))
 412     (build-system cmake-build-system)
 413     (arguments
 414      '(#:tests? #f ;no check target
 415        #:phases
 416        (modify-phases %standard-phases
 417          (add-after 'unpack 'delete-broken-symlinks
 418            (lambda _
 419              (for-each delete-file '("applications/arts/data"
 420                                      "applications/asp/data"
 421                                      "applications/easysvm/data"
 422                                      "applications/msplicer/data"
 423                                      "applications/ocr/data"
 424                                      "examples/documented/data"
 425                                      "examples/documented/matlab_static"
 426                                      "examples/documented/octave_static"
 427                                      "examples/undocumented/data"
 428                                      "examples/undocumented/matlab_static"
 429                                      "examples/undocumented/octave_static"
 430                                      "tests/integration/data"
 431                                      "tests/integration/matlab_static"
 432                                      "tests/integration/octave_static"
 433                                      "tests/integration/python_modular/tests"))
 434              #t))
 435          (add-after 'unpack 'change-R-target-path
 436            (lambda* (#:key outputs #:allow-other-keys)
 437              (substitute* '("src/interfaces/r_modular/CMakeLists.txt"
 438                             "src/interfaces/r_static/CMakeLists.txt"
 439                             "examples/undocumented/r_modular/CMakeLists.txt")
 440                (("\\$\\{R_COMPONENT_LIB_PATH\\}")
 441                 (string-append (assoc-ref outputs "out")
 442                                "/lib/R/library/")))
 443              #t))
 444          (add-after 'unpack 'fix-octave-modules
 445            (lambda* (#:key outputs #:allow-other-keys)
 446              (substitute* '("src/interfaces/octave_modular/CMakeLists.txt"
 447                             "src/interfaces/octave_static/CMakeLists.txt")
 448                (("^include_directories\\(\\$\\{OCTAVE_INCLUDE_DIRS\\}")
 449                 "include_directories(${OCTAVE_INCLUDE_DIRS} ${OCTAVE_INCLUDE_DIRS}/octave"))
 450
 451              ;; change target directory
 452              (substitute* "src/interfaces/octave_modular/CMakeLists.txt"
 453                (("\\$\\{OCTAVE_OCT_LOCAL_API_FILE_DIR\\}")
 454                 (string-append (assoc-ref outputs "out")
 455                                "/share/octave/packages")))
 456              #t))
 457          (add-before 'build 'set-HOME
 458            ;; $HOME needs to be set at some point during the build phase
 459            (lambda _ (setenv "HOME" "/tmp") #t)))
 460        #:configure-flags
 461        (list "-DCMAKE_BUILD_WITH_INSTALL_RPATH=TRUE"
 462              "-DUSE_SVMLIGHT=OFF" ;disable proprietary SVMLIGHT
 463              ;;"-DJavaModular=ON" ;requires unpackaged jblas
 464              ;;"-DRubyModular=ON" ;requires unpackaged ruby-narray
 465              ;;"-DPerlModular=ON" ;"FindPerlLibs" does not exist
 466              ;;"-DLuaModular=ON"  ;fails because lua doesn't build pkgconfig file
 467              "-DOctaveModular=ON"
 468              "-DOctaveStatic=ON"
 469              "-DPythonModular=ON"
 470              "-DPythonStatic=ON"
 471              "-DRModular=ON"
 472              "-DRStatic=ON"
 473              "-DCmdLineStatic=ON")))
 474     (inputs
 475      `(("python" ,python)
 476        ("numpy" ,python-numpy)
 477        ("r-minimal" ,r-minimal)
 478        ("octave" ,octave)
 479        ("swig" ,swig)
 480        ("hdf5" ,hdf5)
 481        ("atlas" ,atlas)
 482        ("arpack" ,arpack-ng)
 483        ("lapack" ,lapack)
 484        ("glpk" ,glpk)
 485        ("libxml2" ,libxml2)
 486        ("lzo" ,lzo)
 487        ("zlib" ,zlib)))
 488     (native-inputs
 489      `(("pkg-config" ,pkg-config)))
 490     ;; Non-portable SSE instructions are used so building fails on platforms
 491     ;; other than x86_64.
 492     (supported-systems '("x86_64-linux"))
 493     (home-page "http://shogun-toolbox.org/")
 494     (synopsis "Machine learning toolbox")
 495     (description
 496      "The Shogun Machine learning toolbox provides a wide range of unified and
 497 efficient Machine Learning (ML) methods.  The toolbox seamlessly allows to
 498 combine multiple data representations, algorithm classes, and general purpose
 499 tools.  This enables both rapid prototyping of data pipelines and extensibility
 500 in terms of new algorithms.")
 501     (license license:gpl3+)))
 502
 503 (define-public r-adaptivesparsity
 504   (package
 505     (name "r-adaptivesparsity")
 506     (version "1.4")
 507     (source (origin
 508               (method url-fetch)
 509               (uri (cran-uri "AdaptiveSparsity" version))
 510               (sha256
 511                (base32
 512                 "1az7isvalf3kmdiycrfl6s9k9xqk22k1mc6rh8v0jmcz402qyq8z"))))
 513     (properties
 514      `((upstream-name . "AdaptiveSparsity")))
 515     (build-system r-build-system)
 516     (arguments
 517      `(#:phases
 518        (modify-phases %standard-phases
 519          (add-after 'unpack 'link-against-armadillo
 520            (lambda _
 521              (substitute* "src/Makevars"
 522                (("PKG_LIBS=" prefix)
 523                 (string-append prefix "-larmadillo"))))))))
 524     (propagated-inputs
 525      `(("r-rcpp" ,r-rcpp)
 526        ("r-rcpparmadillo" ,r-rcpparmadillo)))
 527     (inputs
 528      `(("armadillo" ,armadillo)))
 529     (home-page "https://cran.r-project.org/web/packages/AdaptiveSparsity")
 530     (synopsis "Adaptive sparsity models")
 531     (description
 532      "This package implements the Figueiredo machine learning algorithm for
 533 adaptive sparsity and the Wong algorithm for adaptively sparse gaussian
 534 geometric models.")
 535     (license license:lgpl3+)))
 536
 537 (define-public r-kernlab
 538   (package
 539     (name "r-kernlab")
 540     (version "0.9-25")
 541     (source
 542      (origin
 543        (method url-fetch)
 544        (uri (cran-uri "kernlab" version))
 545        (sha256
 546         (base32
 547          "0qnaq9x3j2xc6jrmmd98wc6hkzch487s4p3a9lnc00xvahkhgpmr"))))
 548     (build-system r-build-system)
 549     (home-page "https://cran.r-project.org/web/packages/kernlab")
 550     (synopsis "Kernel-based machine learning tools")
 551     (description
 552      "This package provides kernel-based machine learning methods for
 553 classification, regression, clustering, novelty detection, quantile regression
 554 and dimensionality reduction.  Among other methods @code{kernlab} includes
 555 Support Vector Machines, Spectral Clustering, Kernel PCA, Gaussian Processes
 556 and a QP solver.")
 557     (license license:gpl2)))
 558
 559 (define-public dlib
 560   (package
 561     (name "dlib")
 562     (version "19.7")
 563     (source (origin
 564               (method url-fetch)
 565               (uri (string-append
 566                     "http://dlib.net/files/dlib-" version ".tar.bz2"))
 567               (sha256
 568                (base32
 569                 "1mljz02kwkrbggyncxv5fpnyjdybw2qihaacb3js8yfkw12vwpc2"))
 570               (modules '((guix build utils)))
 571               (snippet
 572                '(begin
 573                   ;; Delete ~13MB of bundled dependencies.
 574                   (delete-file-recursively "dlib/external")
 575                   (delete-file-recursively "docs/dlib/external")
 576                   #t))))
 577     (build-system cmake-build-system)
 578     (arguments
 579      `(#:phases
 580        (modify-phases %standard-phases
 581          (add-after 'unpack 'disable-asserts
 582            (lambda _
 583              ;; config.h recommends explicitly enabling or disabling asserts
 584              ;; when building as a shared library. By default neither is set.
 585              (substitute* "dlib/config.h"
 586                (("^//#define DLIB_DISABLE_ASSERTS") "#define DLIB_DISABLE_ASSERTS"))
 587              #t))
 588          (add-after 'disable-asserts 'disable-failing-tests
 589            (lambda _
 590              ;; One test times out on MIPS, so we need to disable it.
 591              ;; Others are flaky on some platforms.
 592              (let* ((system ,(or (%current-target-system)
 593                                  (%current-system)))
 594                     (disabled-tests (cond
 595                                      ((string-prefix? "mips64" system)
 596                                       '("object_detector" ; timeout
 597                                         "data_io"))
 598                                      ((string-prefix? "armhf" system)
 599                                       '("learning_to_track"))
 600                                      ((string-prefix? "i686" system)
 601                                       '("optimization"))
 602                                      (else '()))))
 603                (for-each
 604                 (lambda (test)
 605                   (substitute* "dlib/test/makefile"
 606                     (((string-append "SRC \\+= " test "\\.cpp")) "")))
 607                 disabled-tests)
 608                #t)))
 609          (replace 'check
 610            (lambda _
 611              ;; No test target, so we build and run the unit tests here.
 612              (let ((test-dir (string-append "../dlib-" ,version "/dlib/test")))
 613                (with-directory-excursion test-dir
 614                  (and (zero? (system* "make" "-j" (number->string (parallel-job-count))))
 615                       (zero? (system* "./dtest" "--runall")))))))
 616          (add-after 'install 'delete-static-library
 617            (lambda* (#:key outputs #:allow-other-keys)
 618              (delete-file (string-append (assoc-ref outputs "out")
 619                                          "/lib/libdlib.a"))
 620              #t)))))
 621     (native-inputs
 622      `(("pkg-config" ,pkg-config)))
 623     (inputs
 624      `(("giflib" ,giflib)
 625        ("lapack" ,lapack)
 626        ("libjpeg" ,libjpeg)
 627        ("libpng" ,libpng)
 628        ("libx11" ,libx11)
 629        ("openblas" ,openblas)
 630        ("zlib" ,zlib)))
 631     (synopsis
 632      "Toolkit for making machine learning and data analysis applications in C++")
 633     (description
 634      "Dlib is a modern C++ toolkit containing machine learning algorithms and
 635 tools.  It is used in both industry and academia in a wide range of domains
 636 including robotics, embedded devices, mobile phones, and large high performance
 637 computing environments.")
 638     (home-page "http://dlib.net")
 639     (license license:boost1.0)))
 640
 641 (define-public python-scikit-learn
 642   (package
 643     (name "python-scikit-learn")
 644     (version "0.19.1")
 645     (source
 646      (origin
 647        (method url-fetch)
 648        (uri (string-append
 649              "https://github.com/scikit-learn/scikit-learn/archive/"
 650              version ".tar.gz"))
 651        (file-name (string-append name "-" version ".tar.gz"))
 652        (sha256
 653         (base32
 654          "18n8775kyfwbvcjjjzda9c5sqy4737c0hrmj6qj1ps2jmlqzair9"))
 655        (patches (search-patches
 656                 "python-scikit-learn-fix-test-non-determinism.patch"))))
 657     (build-system python-build-system)
 658     (arguments
 659      `(#:phases
 660        (modify-phases %standard-phases
 661          (delete 'check)
 662          (add-after 'install 'check
 663            ;; Running tests from the source directory requires
 664            ;; an "inplace" build with paths relative to CWD.
 665            ;; http://scikit-learn.org/stable/developers/advanced_installation.html#testing
 666            ;; Use the installed version instead.
 667            (lambda* (#:key inputs outputs #:allow-other-keys)
 668              (add-installed-pythonpath inputs outputs)
 669              ;; some tests require access to "$HOME"
 670              (setenv "HOME" "/tmp")
 671              ;; Step out of the source directory just to be sure.
 672              (chdir "..")
 673              (zero? (system* "nosetests" "-v" "sklearn")))))))
 674     (inputs
 675      `(("openblas" ,openblas)))
 676     (native-inputs
 677      `(("python-nose" ,python-nose)
 678        ("python-cython" ,python-cython)))
 679     (propagated-inputs
 680      `(("python-numpy" ,python-numpy)
 681        ("python-scipy" ,python-scipy)))
 682     (home-page "http://scikit-learn.org/")
 683     (synopsis "Machine Learning in Python")
 684     (description
 685      "Scikit-learn provides simple and efficient tools for data
 686 mining and data analysis.")
 687     (license license:bsd-3)))
 688
 689 (define-public python2-scikit-learn
 690   (package-with-python2 python-scikit-learn))